[FieldTrip] Missing resolution Information in *vhdr causes ft_preprocessing to return only NaNs

Wed Jan 25 14:47:26 CET 2012

Julian,

Brainvision Analyzer is somewhat finicky, but I've never seen it do this,
and I don't seem to be able to reproduce the problem here.

If you can get access to the original datasets, then rereferencing in
Fieldtrip might be a solution.

And if you can't get the original datasets, then you could try editing the
header files to include the resolution. I don't think the resolution should
change after rereferencing, so you could simply put the resolution in
there. Alternatively, specifying the resolution
in hdr.orig.resolution should be possible, perhaps with some editing.
Also, since Fieldtrip could open the files earlier, it would stand to
reason that it either 'makes up' some values, doesn't need them (which
would be odd), or somehow deduces them from other values. However, in my
*.vhdr files it specifies the resolution twice, once below [Channel Infos]
and once under [Channels], but nothing I can find that defines it any other
way. So, I'm guessing Fieldtrip used to make them up, but doesn't anymore.
So, placing a resolution in the files or specifying it in Fieldtrip should
not be a problem. Ideally, you would want the original resolution, but if
that's not known, you could try winging it with a value that seems 'close
enough'.

Hope this helps,

Casper van Heck

On Wed, Jan 25, 2012 at 1:49 PM, Karch, Julian <karch at mpib-berlin.mpg.de>wrote:

>  Hi,****
>
> ** **
>
> thanks for your answer. It seems that I was a little imprecise. Of course
> the original data set doesn't change but if I export the a data set after
> setting a new reference in Brainvision Analyzer the header looks like that:
> ****
>
> ** **
>
> Original header real.vhdr****
>
> ===============================****
>
> Brain Vision Data Exchange Header File Version 1.0****
>
> ; Data created by the Vision Recorder****
>
> [...]****
>
> Ch4=Fz,,0.1,µV****
>
> ** **
>
>  realnewRef.vhdr****
>
> ===============================****
>
> Brain Vision Data Exchange Header File Version 1.0****
>
> ; Data created from history path: real/Raw Data/New Reference****
>
> [...]****
>
> Ch4=Fz,Avg,,µV****
>
> ** **
>
> This was just a test I did with some random data. I don't have acess to
> the orginal recording for the data sets I want to read in. The header from
> them look like****
>
> Brain Vision Data Exchange Header File Version 1.0****
>
> ; Data created from history path: passive3101/Raw Data/Filters/New
> Reference/Attentive****
>
> [...]****
>
> Ch12=Fz,ref new,,****
>
> ** **
>
> Like I said what's really strange that I think I was able to preprocess
> the exact same data set a couple of month ago.****
>
> ** **
>
> Thanks for your help!****
>
> ** **
>
> Best,****
>
> ** **
>
> Julian****
>
> ** **
>
> ** **
>
> ** **
>
> ** **
>
> *Von:* fieldtrip-bounces at donders.ru.nl [mailto:
> fieldtrip-bounces at donders.ru.nl] *Im Auftrag von *Casper van Heck
> *Gesendet:* Wednesday, January 25, 2012 10:10 AM
> *An:* Email discussion list for the FieldTrip project
> *Betreff:* Re: [FieldTrip] Missing resolution Information in *vhdr causes
> ft_preprocessing to return only NaNs****
>
> ** **
>
> Julian,****
>
> ** **
>
> It is my understanding that the header file doesn't change at all, since
> Brainvision Analyzer stores all changes either in the 'history' files or
> temporary files in the history folder. The *.vhdr and *.eeg (and marker
> files, if any) should be unchanged after preprocessing. Therefore,
> resolution information should still be there.****
>
> ** **
>
> Could you check the contents of the header file with notepad?****
>
> It should say something like this for every channel under "[Channel
> Infos]":****
>
> Ch27=Fz,,0.0715,ÂµV****
>
> ** **
>
> Also, you could try to open it with Brainvision Analyzer, and see if that
> gives an error of sorts.****
>
> ** **
>
> Sincerely,****
>
> ** **
>
> Casper van Heck****
>
> ** **
>
> On Tue, Jan 24, 2012 at 11:54 PM, Karch, Julian <karch at mpib-berlin.mpg.de>
> wrote:****
>
> Hi,****
>
>  ****
>
> I'm working on a brainvision EEG dataset  which was preprocessed by
> someone else using Brainvision Analyzer. One part of his preprocessing was
> to set a new reference. This processing step makes the resolution
> information in the *vhdr file disappear. Because of that
> hdr.orig.resolution=NaN for all channels.  As result of that the lines****
>
>                 calib = diag(hdr.resolution(chanindx));****
>
>       % using a sparse multiplication speeds it up****
>
>       dat = full(sparse(calib) * dat);****
>
> in read_brainvision_eeg produce only NaN. This again results in trials
> which only contain NaNs.****
>
>  ****
>
> I do weekly updates of fieldtrip using svn. Because I'm quite sure if was
> able to read in, using ft_preprocssing, the excact same dataset, even with
> the same cfg file, earlier this year I checked the modifications for the
> last half year or so but I couldn't find any change which could have broken
> it.****
>
> My two questions are. How would you handle this problem? Just plug in some
> random numbers like 0.1 ? Is this an issue with fieldtrip or am I doing
> something wrong? Were there any changes to the involved functions which
> could have changed the behavior in that way?****
>
>  ****
>
> Thanks in advance!****
>
>  ****
>
> Best,****
>
>  ****
>
> Julian****
>
>  ****
>
> Julian Karch ****
>
> Research Assistant****
>
>  ****
>
> Center for Lifespan Psychology****
>
> MPI for Human Development****
>
> Lentzeallee 94, 14195 Berlin, Germany****
>
> phone: +49-30-82406-296****
>
> fax: +49-30-8249939****
>
> web: http://www.mpib-berlin.mpg.de****
>
>  ****
>
>
> _______________________________________________
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>
> ** **
>
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